I recently came across an article titled DNAproDB: an interactive tool for structural analysis of DNA-protein complexes by Sagendorf et al. in Nucleic Acids Research (NAR). Notably, the DNAproDB tool allows users to search the underlying database by combining features of the DNA, protein, or DNA-protein interactions at the interface. Compared to the well-established NUCPLOT tool which generates only ‘static’ schematic diagrams of protein-nucleic acid interactions, DNAproDB is interactive and more user friendly, with many new features.
Nucleotide-residue interaction geometry (stacking, pseudo-pairing or other) is determined using SNAP, a new component of the 3DNA program suite (35). SNAP also serves as a fall-back for calculating hydrogen bonds if HBPLUS cannot process the file.
I am glad that SNAP has also been used for identifying H-bonds where HBPLUS fails. The H-bonding detection algorithm, initially implemented in 3DNA (v2.3 and before) and refined in DSSR/SNAP, was originally intended to make the 3DNA software fully independent of third-party tools. I did not expect this feature could one day compete with dedicated H-bond finding tools, such as HBPLUS.
By the way, 3DNA is also cited in the DNAproDB NAR paper, as below:
DNA base pairing, shape parameters and conformation are derived from the 3DNA program suite (29) with a 10.0 Å cut-off for helix breaking.